Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
- ======================================================================-====*/
+ ===========================================================================**/
#ifndef CLITKEXTRACTLUNGSFILTER_TXX
#define CLITKEXTRACTLUNGSFILTER_TXX
#include "clitkSetBackgroundImageFilter.h"
#include "clitkSegmentationUtils.h"
#include "clitkAutoCropFilter.h"
-#include "clitkExtractSliceFilter.h"
+#include "clitkCropLikeImageFilter.h"
+#include "clitkFillMaskFilter.h"
+#include "clitkMemoryUsage.h"
// itk
#include "itkBinaryThresholdImageFilter.h"
#include "itkOtsuThresholdImageFilter.h"
#include "itkBinaryThinningImageFilter3D.h"
#include "itkImageIteratorWithIndex.h"
+#include "itkBinaryMorphologicalOpeningImageFilter.h"
+#include "itkBinaryMorphologicalClosingImageFilter.h"
+#include "itkConstantPadImageFilter.h"
//--------------------------------------------------------------------
-template <class ImageType, class MaskImageType>
-clitk::ExtractLungFilter<ImageType, MaskImageType>::
+template <class ImageType>
+clitk::ExtractLungFilter<ImageType>::
ExtractLungFilter():
clitk::FilterBase(),
clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
m_MaxSeedNumber = 500;
// Default global options
- this->SetNumberOfRequiredInputs(2);
+ this->SetNumberOfRequiredInputs(1);
SetPatientMaskBackgroundValue(0);
SetBackgroundValue(0); // Must be zero
SetForegroundValue(1);
SetMinimalComponentSize(100);
+ VerboseRegionGrowingFlagOff();
// Step 1 default values
SetUpperThreshold(-300);
SetMultiplierForTrachea(5);
SetThresholdStepSizeForTrachea(64);
SetNumberOfSlicesToSkipBeforeSearchingSeed(0);
+ TracheaVolumeMustBeCheckedFlagOn();
// Step 3 default values
SetNumberOfHistogramBins(500);
p3->UseLastKeepOff();
SetLabelizeParameters3(p3);
- // Step 5 : find bronchial bifurcations
- FindBronchialBifurcationsOn();
+ // Step 5
+ OpenCloseFlagOff();
+ SetOpenCloseRadius(1);
+
+ // Step 6
+ FillHolesFlagOn();
+ AutoCropOn();
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template <class ImageType, class MaskImageType>
+template <class ImageType>
void
-clitk::ExtractLungFilter<ImageType, MaskImageType>::
+clitk::ExtractLungFilter<ImageType>::
SetInput(const ImageType * image)
{
this->SetNthInput(0, const_cast<ImageType *>(image));
//--------------------------------------------------------------------
-template <class ImageType, class MaskImageType>
+template <class ImageType>
void
-clitk::ExtractLungFilter<ImageType, MaskImageType>::
-SetInputPatientMask(MaskImageType * image, MaskImagePixelType bg )
-{
- this->SetNthInput(1, const_cast<MaskImageType *>(image));
- SetPatientMaskBackgroundValue(bg);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType, class MaskImageType>
-void
-clitk::ExtractLungFilter<ImageType, MaskImageType>::
+clitk::ExtractLungFilter<ImageType>::
AddSeed(InternalIndexType s)
{
m_Seeds.push_back(s);
//--------------------------------------------------------------------
-template <class ImageType, class MaskImageType>
-template<class ArgsInfoType>
+template <class ImageType>
void
-clitk::ExtractLungFilter<ImageType, MaskImageType>::
-SetArgsInfo(ArgsInfoType mArgsInfo)
-{
- SetVerboseOption_GGO(mArgsInfo);
- SetVerboseStep_GGO(mArgsInfo);
- SetWriteStep_GGO(mArgsInfo);
- SetVerboseWarningOff_GGO(mArgsInfo);
-
- SetUpperThreshold_GGO(mArgsInfo);
- SetLowerThreshold_GGO(mArgsInfo);
- SetNumberOfSlicesToSkipBeforeSearchingSeed_GGO(mArgsInfo);
- SetLabelizeParameters1_GGO(mArgsInfo);
- if (!mArgsInfo.remove1_given) {
- GetLabelizeParameters1()->AddLabelToRemove(2);
- if (GetVerboseOption()) VerboseOption("remove1", 2);
- }
-
- SetUpperThresholdForTrachea_GGO(mArgsInfo);
- SetMultiplierForTrachea_GGO(mArgsInfo);
- SetThresholdStepSizeForTrachea_GGO(mArgsInfo);
- AddSeed_GGO(mArgsInfo);
-
- SetMinimalComponentSize_GGO(mArgsInfo);
-
- SetNumberOfHistogramBins_GGO(mArgsInfo);
- SetLabelizeParameters2_GGO(mArgsInfo);
-
- SetRadiusForTrachea_GGO(mArgsInfo);
- SetLabelizeParameters3_GGO(mArgsInfo);
-
- SetAFDBFilename_GGO(mArgsInfo);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType, class MaskImageType>
-void
-clitk::ExtractLungFilter<ImageType, MaskImageType>::
+clitk::ExtractLungFilter<ImageType>::
GenerateOutputInformation()
{
+ clitk::PrintMemory(GetVerboseMemoryFlag(), "Initial memory"); // OK
Superclass::GenerateOutputInformation();
- //this->GetOutput(0)->SetRequestedRegion(this->GetOutput(0)->GetLargestPossibleRegion());
+
+ // Read DB
+ LoadAFDB();
// Get input pointers
- patient = dynamic_cast<const MaskImageType*>(itk::ProcessObject::GetInput(1));
input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
+ patient = GetAFDB()->template GetImage <MaskImageType>("Patient");
+ PrintMemory(GetVerboseMemoryFlag(), "After reading patient"); // OK
+
+ //--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+ // Crop input like patient image (must have the same spacing)
+ // It copy the input if the same are the same
+ StartNewStep("Copy and crop input image to 'patient' extends");
+ typedef clitk::CropLikeImageFilter<ImageType> CropImageFilter;
+ typename CropImageFilter::Pointer cropFilter = CropImageFilter::New();
+ // cropFilter->ReleaseDataFlagOn(); // NO=seg fault !!
+ cropFilter->SetInput(input);
+ cropFilter->SetCropLikeImage(patient);
+ cropFilter->Update();
+ working_input = cropFilter->GetOutput();
+ // cropFilter->Delete(); // NO !!!! if yes, sg fault, Cropfilter is buggy !??
+ StopCurrentStep<ImageType>(working_input);
+ PrintMemory(GetVerboseMemoryFlag(), "After crop"); // OK, slightly more than a copy of input
- // Check image
- if (!HaveSameSizeAndSpacing<ImageType, MaskImageType>(input, patient)) {
- clitkExceptionMacro("the 'input' and 'patient' masks must have the same size & spacing.");
- }
-
//--------------------------------------------------------------------
//--------------------------------------------------------------------
StartNewStep("Set background to initial image");
working_input = SetBackground<ImageType, MaskImageType>
- (input, patient, GetPatientMaskBackgroundValue(), -1000);
+ (working_input, patient, GetPatientMaskBackgroundValue(), -1000, true);
+
+ // Pad images with air to prevent patient touching the image border
+ static const unsigned int Dim = ImageType::ImageDimension;
+ typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
+ typename PadFilterType::Pointer padFilter = PadFilterType::New();
+ padFilter->SetInput(working_input);
+ padFilter->SetConstant(-1000);
+ typename ImageType::SizeType bounds;
+ for (unsigned i = 0; i < Dim - 1; ++i)
+ bounds[i] = 1;
+ bounds[Dim - 1] = 0;
+ padFilter->SetPadLowerBound(bounds);
+ padFilter->SetPadUpperBound(bounds);
+ padFilter->Update();
+ working_input = padFilter->GetOutput();
+
StopCurrentStep<ImageType>(working_input);
+ PrintMemory(GetVerboseMemoryFlag(), "After set bg"); // OK, additional mem = 0
+
+ /*
+ // We do not need patient mask anymore, release memory
+ GetAFDB()->template ReleaseImage<MaskImageType>("Patient");
+ DD(patient->GetReferenceCount());
+ PrintMemory(GetVerboseMemoryFlag(), "After delete patient"); // OK, additional mem = 0
+ patient->Delete();
+ PrintMemory(GetVerboseMemoryFlag(), "After delete patient"); // OK, additional mem = 0
+ */
//--------------------------------------------------------------------
//--------------------------------------------------------------------
}
}
// Threshold to get air
- typedef itk::BinaryThresholdImageFilter<ImageType, InternalImageType> InputBinarizeFilterType;
- typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New();
+ typedef itk::BinaryThresholdImageFilter<ImageType, MaskImageType> InputBinarizeFilterType;
+ typename InputBinarizeFilterType::Pointer binarizeFilter = InputBinarizeFilterType::New();
binarizeFilter->SetInput(working_input);
if (m_UseLowerThreshold) binarizeFilter->SetLowerThreshold(m_LowerThreshold);
+ // binarizeFilter->CanRunInPlace() is false
binarizeFilter->SetUpperThreshold(m_UpperThreshold);
- binarizeFilter ->SetInsideValue(this->GetForegroundValue());
- binarizeFilter ->SetOutsideValue(this->GetBackgroundValue());
+ binarizeFilter->SetInsideValue(this->GetForegroundValue());
+ binarizeFilter->SetOutsideValue(this->GetBackgroundValue());
binarizeFilter->Update();
- working_image = binarizeFilter->GetOutput();
-
- // Labelize and keep right labels
- working_image = Labelize<InternalImageType>(working_image, GetBackgroundValue(), true, GetMinimalComponentSize());
+ working_mask = binarizeFilter->GetOutput();
+ PrintMemory(GetVerboseMemoryFlag(), "After Binarizefilter"); // OK, additional mem is one mask image
- working_image = RemoveLabels<InternalImageType>
- (working_image, GetBackgroundValue(), GetLabelizeParameters1()->GetLabelsToRemove());
+ // Labelize and keep right labels
+ working_mask =
+ Labelize<MaskImageType>
+ (working_mask, GetBackgroundValue(), true, GetMinimalComponentSize());
+ PrintMemory(GetVerboseMemoryFlag(), "After Labelize"); // BUG ? additional mem around 1 time the input ?
+
+ working_mask = RemoveLabels<MaskImageType>
+ (working_mask, GetBackgroundValue(), GetLabelizeParameters1()->GetLabelsToRemove());
+ PrintMemory(GetVerboseMemoryFlag(), "After RemoveLabels"); // OK additional mem = 0
- typename InternalImageType::Pointer air = KeepLabels<InternalImageType>
- (working_image,
+ working_mask = KeepLabels<MaskImageType>
+ (working_mask,
GetBackgroundValue(),
GetForegroundValue(),
GetLabelizeParameters1()->GetFirstKeep(),
GetLabelizeParameters1()->GetLastKeep(),
GetLabelizeParameters1()->GetUseLastKeep());
+ PrintMemory(GetVerboseMemoryFlag(), "After KeepLabels to create the 'air'");
// Set Air to BG
- working_input = SetBackground<ImageType, InternalImageType>
- (working_input, air, this->GetForegroundValue(), this->GetBackgroundValue());
+ working_input = SetBackground<ImageType, MaskImageType>
+ (working_input, working_mask, this->GetForegroundValue(), this->GetBackgroundValue(), true);
+ PrintMemory(GetVerboseMemoryFlag(), "After SetBackground");
// End
StopCurrentStep<ImageType>(working_input);
//--------------------------------------------------------------------
StartNewStep("Search for the trachea");
SearchForTrachea();
+ PrintMemory(GetVerboseMemoryFlag(), "After SearchForTrachea");
//--------------------------------------------------------------------
//--------------------------------------------------------------------
StartNewStep("Extract the lung with Otsu filter");
// Automated Otsu thresholding and relabeling
- typedef itk::OtsuThresholdImageFilter<ImageType,InternalImageType> OtsuThresholdImageFilterType;
+ typedef itk::OtsuThresholdImageFilter<ImageType,MaskImageType> OtsuThresholdImageFilterType;
typename OtsuThresholdImageFilterType::Pointer otsuFilter=OtsuThresholdImageFilterType::New();
otsuFilter->SetInput(working_input);
otsuFilter->SetNumberOfHistogramBins(GetNumberOfHistogramBins());
otsuFilter->SetInsideValue(this->GetForegroundValue());
otsuFilter->SetOutsideValue(this->GetBackgroundValue());
otsuFilter->Update();
- working_image = otsuFilter->GetOutput();
+ working_mask = otsuFilter->GetOutput();
// Set output
- StopCurrentStep<InternalImageType>(working_image);
+ StopCurrentStep<MaskImageType>(working_mask);
+ PrintMemory(GetVerboseMemoryFlag(), "After Otsufilter");
//--------------------------------------------------------------------
//--------------------------------------------------------------------
StartNewStep("Select labels");
// Keep right labels
- working_image = LabelizeAndSelectLabels<InternalImageType>
- (working_image,
+ working_mask = LabelizeAndSelectLabels<MaskImageType>
+ (working_mask,
GetBackgroundValue(),
GetForegroundValue(),
false,
GetLabelizeParameters2());
// Set output
- StopCurrentStep<InternalImageType>(working_image);
+ StopCurrentStep<MaskImageType>(working_mask);
+ PrintMemory(GetVerboseMemoryFlag(), "After LabelizeAndSelectLabels");
//--------------------------------------------------------------------
//--------------------------------------------------------------------
if (m_Seeds.size() != 0) { // if ==0 ->no trachea found
StartNewStep("Remove the trachea");
// Set the trachea
- working_image = SetBackground<InternalImageType, InternalImageType>
- (working_image, trachea_tmp, 1, -1);
+ working_mask = SetBackground<MaskImageType, MaskImageType>
+ (working_mask, trachea, 1, -1, true);
+ PrintMemory(GetVerboseMemoryFlag(), "After SetBackground");
// Dilate the trachea
static const unsigned int Dim = ImageType::ImageDimension;
KernelType structuringElement;
structuringElement.SetRadius(GetRadiusForTrachea());
structuringElement.CreateStructuringElement();
- typedef clitk::ConditionalBinaryDilateImageFilter<InternalImageType, InternalImageType, KernelType> ConditionalBinaryDilateImageFilterType;
+ typedef clitk::ConditionalBinaryDilateImageFilter<MaskImageType, MaskImageType, KernelType> ConditionalBinaryDilateImageFilterType;
typename ConditionalBinaryDilateImageFilterType::Pointer dilateFilter = ConditionalBinaryDilateImageFilterType::New();
dilateFilter->SetBoundaryToForeground(false);
dilateFilter->SetKernel(structuringElement);
dilateFilter->SetBackgroundValue (1);
dilateFilter->SetForegroundValue (-1);
- dilateFilter->SetInput (working_image);
+ dilateFilter->SetInput (working_mask);
dilateFilter->Update();
- working_image = dilateFilter->GetOutput();
+ working_mask = dilateFilter->GetOutput();
+ PrintMemory(GetVerboseMemoryFlag(), "After dilate");
// Set trachea with dilatation
- trachea_tmp = SetBackground<InternalImageType, InternalImageType>
- (trachea_tmp, working_image, -1, this->GetForegroundValue());
+ trachea = SetBackground<MaskImageType, MaskImageType>
+ (trachea, working_mask, -1, this->GetForegroundValue(), true);
// Remove the trachea
- working_image = SetBackground<InternalImageType, InternalImageType>
- (working_image, working_image, -1, this->GetBackgroundValue());
+ working_mask = SetBackground<MaskImageType, MaskImageType>
+ (working_mask, working_mask, -1, this->GetBackgroundValue(), true);
// Label
- working_image = LabelizeAndSelectLabels<InternalImageType>
- (working_image,
+ working_mask = LabelizeAndSelectLabels<MaskImageType>
+ (working_mask,
GetBackgroundValue(),
GetForegroundValue(),
false,
GetLabelizeParameters3());
// Set output
- StopCurrentStep<InternalImageType>(working_image);
+ StopCurrentStep<MaskImageType>(working_mask);
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
- typedef clitk::AutoCropFilter<InternalImageType> CropFilterType;
- typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ PrintMemory(GetVerboseMemoryFlag(), "before autocropfilter");
if (m_Seeds.size() != 0) { // if ==0 ->no trachea found
- StartNewStep("Croping trachea");
- cropFilter->SetInput(trachea_tmp);
- cropFilter->Update(); // Needed
- typedef itk::CastImageFilter<InternalImageType, MaskImageType> CastImageFilterType;
- typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
- caster->SetInput(cropFilter->GetOutput());
- caster->Update();
- trachea = caster->GetOutput();
+ if (GetAutoCrop())
+ trachea = clitk::AutoCrop<MaskImageType>(trachea, GetBackgroundValue());
+ else
+ {
+ // Remove Padding region
+ typedef itk::CropImageFilter<MaskImageType, MaskImageType> CropFilterType;
+ typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ cropFilter->SetInput(trachea);
+ cropFilter->SetLowerBoundaryCropSize(bounds);
+ cropFilter->SetUpperBoundaryCropSize(bounds);
+ cropFilter->Update();
+ trachea = cropFilter->GetOutput();
+ }
StopCurrentStep<MaskImageType>(trachea);
+ PrintMemory(GetVerboseMemoryFlag(), "after delete trachea");
}
+ PrintMemory(GetVerboseMemoryFlag(), "after delete trachea");
//--------------------------------------------------------------------
//--------------------------------------------------------------------
- StartNewStep("Croping lung");
- typename CropFilterType::Pointer cropFilter2 = CropFilterType::New(); // Needed to reset pipeline
- cropFilter2->SetInput(working_image);
- cropFilter2->Update();
- working_image = cropFilter2->GetOutput();
- StopCurrentStep<InternalImageType>(working_image);
+ StartNewStep("Cropping lung");
+ PrintMemory(GetVerboseMemoryFlag(), "Before Autocropfilter");
+ if (GetAutoCrop())
+ working_mask = clitk::AutoCrop<MaskImageType>(working_mask, GetBackgroundValue());
+ else
+ {
+ // Remove Padding region
+ typedef itk::CropImageFilter<MaskImageType, MaskImageType> CropFilterType;
+ typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ cropFilter->SetInput(working_mask);
+ cropFilter->SetLowerBoundaryCropSize(bounds);
+ cropFilter->SetUpperBoundaryCropSize(bounds);
+ cropFilter->Update();
+ working_mask = cropFilter->GetOutput();
+ }
+ StopCurrentStep<MaskImageType>(working_mask);
+
+ //--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+ // Final OpenClose
+ if (GetOpenCloseFlag()) {
+ StartNewStep("Open/Close");
+ PrintMemory(GetVerboseMemoryFlag(), "Before OpenClose");
+
+ // Structuring element
+ typedef itk::BinaryBallStructuringElement<InternalPixelType, ImageDimension> KernelType;
+ KernelType structuringElement;
+ structuringElement.SetRadius(GetOpenCloseRadius());
+ structuringElement.CreateStructuringElement();
+
+ // Open
+ typedef itk::BinaryMorphologicalOpeningImageFilter<MaskImageType, InternalImageType, KernelType> OpenFilterType;
+ typename OpenFilterType::Pointer openFilter = OpenFilterType::New();
+ openFilter->SetInput(working_mask);
+ openFilter->SetBackgroundValue(GetBackgroundValue());
+ openFilter->SetForegroundValue(GetForegroundValue());
+ openFilter->SetKernel(structuringElement);
+
+ // Close
+ typedef itk::BinaryMorphologicalClosingImageFilter<MaskImageType, MaskImageType, KernelType> CloseFilterType;
+ typename CloseFilterType::Pointer closeFilter = CloseFilterType::New();
+ closeFilter->SetInput(openFilter->GetOutput());
+ closeFilter->SetSafeBorder(true);
+ closeFilter->SetForegroundValue(GetForegroundValue());
+ closeFilter->SetKernel(structuringElement);
+ closeFilter->Update();
+ working_mask = closeFilter->GetOutput();
+ }
+
+ //--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+ // Fill Lungs
+ if (GetFillHolesFlag()) {
+ StartNewStep("Fill Holes");
+ PrintMemory(GetVerboseMemoryFlag(), "Before Fill Holes");
+ typedef clitk::FillMaskFilter<MaskImageType> FillMaskFilterType;
+ typename FillMaskFilterType::Pointer fillMaskFilter = FillMaskFilterType::New();
+ fillMaskFilter->SetInput(working_mask);
+ fillMaskFilter->AddDirection(2);
+ //fillMaskFilter->AddDirection(1);
+ fillMaskFilter->Update();
+ working_mask = fillMaskFilter->GetOutput();
+ StopCurrentStep<MaskImageType>(working_mask);
+ }
//--------------------------------------------------------------------
//--------------------------------------------------------------------
StartNewStep("Separate Left/Right lungs");
+ PrintMemory(GetVerboseMemoryFlag(), "Before Separate");
// Initial label
- working_image = Labelize<InternalImageType>(working_image,
- GetBackgroundValue(),
- false,
- GetMinimalComponentSize());
+ working_mask = Labelize<MaskImageType>(working_mask,
+ GetBackgroundValue(),
+ false,
+ GetMinimalComponentSize());
+
+ PrintMemory(GetVerboseMemoryFlag(), "After Labelize");
// Count the labels
- typedef itk::StatisticsImageFilter<InternalImageType> StatisticsImageFilterType;
+ typedef itk::StatisticsImageFilter<MaskImageType> StatisticsImageFilterType;
typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
- statisticsImageFilter->SetInput(working_image);
+ statisticsImageFilter->SetInput(working_mask);
statisticsImageFilter->Update();
unsigned int initialNumberOfLabels = statisticsImageFilter->GetMaximum();
- working_image = statisticsImageFilter->GetOutput();
+ working_mask = statisticsImageFilter->GetOutput();
+
+ PrintMemory(GetVerboseMemoryFlag(), "After count label");
// Decompose the first label
- static const unsigned int Dim = ImageType::ImageDimension;
if (initialNumberOfLabels<2) {
// Structuring element radius
typename ImageType::SizeType radius;
for (unsigned int i=0;i<Dim;i++) radius[i]=1;
- typedef clitk::DecomposeAndReconstructImageFilter<InternalImageType,InternalImageType> DecomposeAndReconstructFilterType;
+ typedef clitk::DecomposeAndReconstructImageFilter<MaskImageType,MaskImageType> DecomposeAndReconstructFilterType;
typename DecomposeAndReconstructFilterType::Pointer decomposeAndReconstructFilter=DecomposeAndReconstructFilterType::New();
- decomposeAndReconstructFilter->SetInput(working_image);
+ decomposeAndReconstructFilter->SetInput(working_mask);
decomposeAndReconstructFilter->SetVerbose(false);
decomposeAndReconstructFilter->SetRadius(radius);
decomposeAndReconstructFilter->SetMaximumNumberOfLabels(2);
decomposeAndReconstructFilter->SetFullyConnected(true);
decomposeAndReconstructFilter->SetNumberOfNewLabels(1);
decomposeAndReconstructFilter->Update();
- working_image = decomposeAndReconstructFilter->GetOutput();
+ working_mask = decomposeAndReconstructFilter->GetOutput();
}
+ PrintMemory(GetVerboseMemoryFlag(), "After decomposeAndReconstructFilter");
// Retain labels ('1' is largset lung, so right. '2' is left)
- typedef itk::ThresholdImageFilter<InternalImageType> ThresholdImageFilterType;
+ typedef itk::ThresholdImageFilter<MaskImageType> ThresholdImageFilterType;
typename ThresholdImageFilterType::Pointer thresholdFilter = ThresholdImageFilterType::New();
- thresholdFilter->SetInput(working_image);
+ thresholdFilter->SetInput(working_mask);
thresholdFilter->ThresholdAbove(2);
thresholdFilter->SetOutsideValue(this->GetBackgroundValue());
thresholdFilter->Update();
- working_image = thresholdFilter->GetOutput();
- StopCurrentStep<InternalImageType> (working_image);
-
- // Final Cast
- StartNewStep("Cast the lung mask");
- typedef itk::CastImageFilter<InternalImageType, MaskImageType> CastImageFilterType;
- typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
- caster->SetInput(working_image);
- caster->Update();
- output = caster->GetOutput();
+ working_mask = thresholdFilter->GetOutput();
+ StopCurrentStep<MaskImageType> (working_mask);
+ PrintMemory(GetVerboseMemoryFlag(), "After Thresholdfilter");
// Update output info
- this->GetOutput(0)->SetRegions(output->GetLargestPossibleRegion());
+ // output = working_mask;
+ //this->GetOutput(0)->SetRegions(output->GetLargestPossibleRegion());
- // Try to extract bifurcation in the trachea (bronchi)
- if (m_Seeds.size() != 0) { // if ==0 ->no trachea found
+ // this->GetOutput(0)->SetRegions(working_mask->GetLargestPossibleRegion());
- if (GetFindBronchialBifurcations()) {
- StartNewStep("Find bronchial bifurcations");
- // Step 1 : extract skeleton
- typedef itk::BinaryThinningImageFilter3D<MaskImageType, MaskImageType> ThinningFilterType;
- typename ThinningFilterType::Pointer thinningFilter = ThinningFilterType::New();
- thinningFilter->SetInput(trachea);
- thinningFilter->Update();
- typename MaskImageType::Pointer skeleton = thinningFilter->GetOutput();
-
- // Step 2.1 : find first point for tracking
- typedef itk::ImageRegionConstIteratorWithIndex<MaskImageType> IteratorType;
- IteratorType it(skeleton, skeleton->GetLargestPossibleRegion());
- it.GoToReverseBegin();
- while ((!it.IsAtEnd()) && (it.Get() == GetBackgroundValue())) {
- --it;
- }
- if (it.IsAtEnd()) {
- clitkExceptionMacro("first point in the trachea skeleton not found.");
- }
- typename MaskImageType::IndexType index = it.GetIndex();
-
- // Step 2.2 : initialize neighborhooditerator
- typedef itk::NeighborhoodIterator<MaskImageType> NeighborhoodIteratorType;
- typename NeighborhoodIteratorType::SizeType radius;
- radius.Fill(1);
- NeighborhoodIteratorType nit(radius, skeleton, skeleton->GetLargestPossibleRegion());
-
- // Find first label number (must be different from BG and FG)
- typename MaskImageType::PixelType label = GetForegroundValue()+1;
- while ((label == GetBackgroundValue()) || (label == GetForegroundValue())) { label++; }
-
- // Track from the first point
- std::vector<BifurcationType> listOfBifurcations;
- m_SkeletonTree.set_head(index);
- TrackFromThisIndex(listOfBifurcations, skeleton, index, label, m_SkeletonTree.begin());
- DD("end track");
- DD(listOfBifurcations.size());
- DD(m_SkeletonTree.size());
-
- for(unsigned int i=0; i<listOfBifurcations.size(); i++) {
- skeleton->TransformIndexToPhysicalPoint(listOfBifurcations[i].index,
- listOfBifurcations[i].point);
- }
-
- // Search for the first slice that separate the bronchus (carena)
- typedef clitk::ExtractSliceFilter<MaskImageType> ExtractSliceFilterType;
- typename ExtractSliceFilterType::Pointer extractSliceFilter = ExtractSliceFilterType::New();
- extractSliceFilter->SetInput(trachea);
- extractSliceFilter->SetDirection(2);
- extractSliceFilter->Update();
- typedef typename ExtractSliceFilterType::SliceType SliceType;
- std::vector<typename SliceType::Pointer> mInputSlices;
- extractSliceFilter->GetOutputSlices(mInputSlices);
-
- bool stop = false;
- DD(listOfBifurcations[0].index);
- DD(listOfBifurcations[1].index);
- int slice_index = listOfBifurcations[0].index[2]; // first slice from carena in skeleton
- int i=0;
- TreeIterator firstIter = m_SkeletonTree.child(listOfBifurcations[1].treeIter, 0);
- TreeIterator secondIter = m_SkeletonTree.child(listOfBifurcations[1].treeIter, 1);
- typename SliceType::IndexType in1;
- typename SliceType::IndexType in2;
- while (!stop) {
- DD(slice_index);
-
- // Labelize the current slice
- typename SliceType::Pointer temp = Labelize<SliceType>(mInputSlices[slice_index],
- GetBackgroundValue(),
- true,
- GetMinimalComponentSize());
- // Check the value of the two skeleton points;
- in1[0] = (*firstIter)[0];
- in1[1] = (*firstIter)[1];
- typename SliceType::PixelType v1 = temp->GetPixel(in1);
- DD(in1);
- DD((int)v1);
- in2[0] = (*secondIter)[0];
- in2[1] = (*secondIter)[1];
- typename SliceType::PixelType v2 = temp->GetPixel(in2);
- DD(in2);
- DD((int)v2);
-
- // TODO IF NOT FOUND ????
-
- if (v1 != v2) {
- stop = true;
- }
- else {
- i++;
- --slice_index;
- ++firstIter;
- ++secondIter;
- }
- }
- MaskImageIndexType carena_index;
- carena_index[0] = lrint(in2[0] + in1[0])/2.0;
- carena_index[1] = lrint(in2[1] + in1[1])/2.0;
- carena_index[2] = slice_index;
- MaskImagePointType carena_position;
- DD(carena_index);
- skeleton->TransformIndexToPhysicalPoint(carena_index,
- carena_position);
- DD(carena_position);
-
- // Set and save Carina position
- StartNewStep("Save carina position");
- // Try to load the DB
- try {
- LoadAFDB();
- } catch (clitk::ExceptionObject e) {
- // Do nothing if not found, it will be used anyway to write the result
- }
- GetAFDB()->SetPoint3D("Carena", carena_position);
- }
- }
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template <class ImageType, class MaskImageType>
+template <class TImageType>
void
-clitk::ExtractLungFilter<ImageType, MaskImageType>::
-GenerateData()
-{
- // If everything goes well, set the output
- this->GraftOutput(output); // not SetNthOutput
+clitk::ExtractLungFilter<TImageType>::
+GenerateInputRequestedRegion() {
+ // DD("GenerateInputRequestedRegion (nothing?)");
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template <class ImageType, class MaskImageType>
+template <class ImageType>
void
-clitk::ExtractLungFilter<ImageType, MaskImageType>::
-TrackFromThisIndex(std::vector<BifurcationType> & listOfBifurcations,
- MaskImagePointer skeleton,
- MaskImageIndexType index,
- MaskImagePixelType label,
- TreeIterator currentNode)
+clitk::ExtractLungFilter<ImageType>::
+GenerateData()
{
- // Create NeighborhoodIterator
- typedef itk::NeighborhoodIterator<MaskImageType> NeighborhoodIteratorType;
- typename NeighborhoodIteratorType::SizeType radius;
- radius.Fill(1);
- NeighborhoodIteratorType nit(radius, skeleton, skeleton->GetLargestPossibleRegion());
-
- // Track
- std::vector<typename NeighborhoodIteratorType::IndexType> listOfTrackedPoint;
- bool stop = false;
- while (!stop) {
- nit.SetLocation(index);
- nit.SetCenterPixel(label);
- listOfTrackedPoint.clear();
- for(unsigned int i=0; i<nit.Size(); i++) {
- if (i != nit.GetCenterNeighborhoodIndex ()) { // Do not observe the current point
- if (nit.GetPixel(i) == GetForegroundValue()) { // if this is foreground, we continue the tracking
- listOfTrackedPoint.push_back(nit.GetIndex(i));
- }
- }
- }
- if (listOfTrackedPoint.size() == 1) {
- // Add this point to the current path
- currentNode = m_SkeletonTree.append_child(currentNode, listOfTrackedPoint[0]);
- index = listOfTrackedPoint[0];
- }
- else {
- if (listOfTrackedPoint.size() == 2) {
- // m_SkeletonTree->Add(listOfTrackedPoint[0], index); // the parent is 'index'
- // m_SkeletonTree->Add(listOfTrackedPoint[1], index); // the parent is 'index'
- BifurcationType bif(index, label, label+1, label+2);
- bif.treeIter = currentNode;
- listOfBifurcations.push_back(bif);
- TreeIterator firstNode = m_SkeletonTree.append_child(currentNode, listOfTrackedPoint[0]);
- TreeIterator secondNode = m_SkeletonTree.append_child(currentNode, listOfTrackedPoint[1]);
- TrackFromThisIndex(listOfBifurcations, skeleton, listOfTrackedPoint[0], label+1, firstNode);
- TrackFromThisIndex(listOfBifurcations, skeleton, listOfTrackedPoint[1], label+2, secondNode);
- }
- else {
- if (listOfTrackedPoint.size() > 2) {
- clitkExceptionMacro("error while tracking trachea bifurcation. Too much bifurcation points ... ?");
- }
- // Else this it the end of the tracking
- }
- stop = true;
- }
- }
+ // Set the output
+ // this->GraftOutput(output); // not SetNthOutput
+ this->GraftOutput(working_mask); // not SetNthOutput
+ // Store image filenames into AFDB
+ GetAFDB()->SetImageFilename("Lungs", this->GetOutputLungFilename());
+ GetAFDB()->SetImageFilename("Trachea", this->GetOutputTracheaFilename());
+ WriteAFDB();
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template <class ImageType, class MaskImageType>
+template <class ImageType>
bool
-clitk::ExtractLungFilter<ImageType, MaskImageType>::
+clitk::ExtractLungFilter<ImageType>::
SearchForTracheaSeed(int skip)
{
if (m_Seeds.size() == 0) { // try to find seed (if not zero, it is given by user)
// if we do not found : restart
stop = (m_Seeds.size() != 0);
if (!stop) {
- if (GetVerboseStep()) {
+ if (GetVerboseStepFlag()) {
std::cout << "\t No seed found this time. I skip some slices and restart." << std::endl;
}
if (skip > 0.5 * working_input->GetLargestPossibleRegion().GetSize()[2]) {
}
skip += 5;
}
+ else {
+ // DD(m_Seeds[0]);
+ // DD(m_Seeds.size());
+ }
}
}
return (m_Seeds.size() != 0);
//--------------------------------------------------------------------
-template <class ImageType, class MaskImageType>
+template <class ImageType>
void
-clitk::ExtractLungFilter<ImageType, MaskImageType>::
+clitk::ExtractLungFilter<ImageType>::
TracheaRegionGrowing()
{
// Explosion controlled region growing
- typedef clitk::ExplosionControlledThresholdConnectedImageFilter<ImageType, InternalImageType> ImageFilterType;
+ PrintMemory(GetVerboseMemoryFlag(), "Before ExplosionControlledThresholdConnectedImageFilter");
+ typedef clitk::ExplosionControlledThresholdConnectedImageFilter<ImageType, MaskImageType> ImageFilterType;
typename ImageFilterType::Pointer f= ImageFilterType::New();
f->SetInput(working_input);
- f->SetVerbose(false);
f->SetLower(-2000);
f->SetUpper(GetUpperThresholdForTrachea());
f->SetMinimumLowerThreshold(-2000);
- f->SetMaximumUpperThreshold(0);
+ // f->SetMaximumUpperThreshold(0); // MAYBE TO CHANGE ???
+ f->SetMaximumUpperThreshold(-800); // MAYBE TO CHANGE ???
f->SetAdaptLowerBorder(false);
f->SetAdaptUpperBorder(true);
f->SetMinimumSize(5000);
f->SetMultiplier(GetMultiplierForTrachea());
f->SetThresholdStepSize(GetThresholdStepSizeForTrachea());
f->SetMinimumThresholdStepSize(1);
+ f->SetVerbose(GetVerboseRegionGrowingFlag());
for(unsigned int i=0; i<m_Seeds.size();i++) {
f->AddSeed(m_Seeds[i]);
// DD(m_Seeds[i]);
}
f->Update();
-
+ PrintMemory(GetVerboseMemoryFlag(), "After RG update");
+
// take first (main) connected component
- trachea_tmp = Labelize<InternalImageType>(f->GetOutput(),
- GetBackgroundValue(),
- true,
- GetMinimalComponentSize());
- trachea_tmp = KeepLabels<InternalImageType>(trachea_tmp,
+ trachea = Labelize<MaskImageType>(f->GetOutput(),
+ GetBackgroundValue(),
+ true,
+ 1000);//GetMinimalComponentSize());
+ PrintMemory(GetVerboseMemoryFlag(), "After Labelize");
+ trachea = KeepLabels<MaskImageType>(trachea,
GetBackgroundValue(),
GetForegroundValue(),
1, 1, false);
+ PrintMemory(GetVerboseMemoryFlag(), "After KeepLabels");
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template <class ImageType, class MaskImageType>
+template <class ImageType>
double
-clitk::ExtractLungFilter<ImageType, MaskImageType>::
+clitk::ExtractLungFilter<ImageType>::
ComputeTracheaVolume()
{
typedef itk::ImageRegionConstIterator<InternalImageType> IteratorType;
- IteratorType iter(trachea_tmp, trachea_tmp->GetLargestPossibleRegion());
+ IteratorType iter(trachea, trachea->GetLargestPossibleRegion());
iter.GoToBegin();
double volume = 0.0;
while (!iter.IsAtEnd()) {
++iter;
}
- double voxelsize = trachea_tmp->GetSpacing()[0]*trachea_tmp->GetSpacing()[1]*trachea_tmp->GetSpacing()[2];
+ double voxelsize = trachea->GetSpacing()[0]*trachea->GetSpacing()[1]*trachea->GetSpacing()[2];
return volume*voxelsize;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template <class ImageType, class MaskImageType>
-void
-clitk::ExtractLungFilter<ImageType, MaskImageType>::
+template <class ImageType>
+void
+clitk::ExtractLungFilter<ImageType>::
SearchForTrachea()
{
// Search for seed among n slices, skip some slices before starting
double volume = 0.0;
int skip = GetNumberOfSlicesToSkipBeforeSearchingSeed();
while (!stop) {
- stop = SearchForTracheaSeed(skip);
- if (stop) {
+ stop = true;
+ if (SearchForTracheaSeed(skip)) {
TracheaRegionGrowing();
volume = ComputeTracheaVolume()/1000; // assume mm3, so divide by 1000 to get cc
- if ((volume > 10) && (volume < 55 )) { // it is ok
- // Typical volume 22.59 cm 3 (± 7.69 cm 3 ) [ Leader 2004 ]
- if (GetVerboseStep()) {
- std::cout << "\t Found trachea with volume " << volume << " cc." << std::endl;
- }
- stop = true;
+ if (GetWriteStepFlag()) {
+ writeImage<MaskImageType>(trachea, "step-trachea-"+toString(skip)+".mhd");
+ }
+ if (GetTracheaVolumeMustBeCheckedFlag()) {
+ if ((volume > 10) && (volume < 65 )) { // depend on image size ...
+ // Typical volume 22.59 cm 3 (± 7.69 cm 3 ) [ Leader 2004 ]
+ if (GetVerboseStepFlag()) {
+ std::cout << "\t Found trachea with volume " << volume << " cc." << std::endl;
+ }
+ }
+ else {
+ if (GetVerboseStepFlag()) {
+ std::cout << "\t The volume of the trachea (" << volume
+ << " cc) seems not correct. I skip some slices (" << skip << ") and restart to find seeds."
+ << std::endl;
+ }
+ skip += 5;
+ stop = false;
+ // empty the list of seed
+ m_Seeds.clear();
+ }
+ if (skip > 0.5 * working_input->GetLargestPossibleRegion().GetSize()[2]) {
+ // we want to skip more than a half of the image, it is probably a bug
+ std::cerr << "2 : Number of slices to skip to find trachea too high = " << skip << std::endl;
+ stop = true;
+ }
}
else {
- if (GetVerboseStep()) {
- std::cout << "\t The volume of the trachea (" << volume
- << " cc) seems not correct. I skip some slices (" << skip << ") and restart to find seeds."
- << std::endl;
- }
- skip += 5;
- stop = false;
- // empty the list of seed
- m_Seeds.clear();
+ stop = true;
}
}
}
if (volume != 0.0) {
// Set output
- StopCurrentStep<InternalImageType>(trachea_tmp);
+ StopCurrentStep<MaskImageType>(trachea);
}
else { // Trachea not found
this->SetWarning("* WARNING * No seed found for trachea.");
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff